Contacts of the strand formed by residues 64 - 72 (chain C) in PDB entry 5Z8N
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 64 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 4.9 8.7 - - + -
22C TYR* 3.7 39.5 - - + -
56C ILE* 4.0 15.7 - - + -
57C GLU 3.3 12.8 - - - +
58C ALA* 4.3 9.6 - - + -
62C ASN 3.5 11.7 - - - +
63C ASN* 1.3 77.4 - - - +
65C LYS* 1.3 69.4 + - - +
66C VAL* 5.1 0.2 - - + -
100C SER* 3.2 10.4 + - - -
101C ALA* 3.0 26.0 + - + +
102C HIS* 5.1 7.6 - - + -
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Residues in contact with LYS 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C GLU* 2.5 39.3 + - + +
59C ASP* 6.0 4.5 - - + +
63C ASN* 5.0 10.3 - - + +
64C VAL* 1.3 81.1 - - - +
66C VAL* 1.3 67.1 + - - +
67C HIS* 5.2 0.4 - - + -
98C VAL* 4.5 19.1 + - + +
99C GLN* 3.9 9.1 - - - +
100C SER* 3.9 28.7 - - - +
101C ALA 4.2 0.2 - - - +
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Residues in contact with VAL 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C TYR* 5.9 1.6 - - + -
31C VAL* 6.3 0.4 - - + -
37C VAL* 6.0 0.9 - - + -
39C MET* 3.9 24.0 - - + -
53C VAL* 4.4 12.6 - - + -
55C LYS 3.6 6.3 - - - +
56C ILE* 4.1 24.2 - - + -
65C LYS* 1.3 80.4 - - - +
67C HIS* 1.3 65.0 + - - +
68C CYS* 3.9 6.3 + - + -
98C VAL* 3.3 5.2 - - - +
99C GLN 2.9 44.2 + - - +
100C SER 4.9 2.0 - - - +
101C ALA* 4.6 10.5 - - + -
104C ILE* 4.4 23.1 - - + -
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Residues in contact with HIS 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ARG* 6.3 0.2 - - - -
53C VAL* 3.7 4.5 - - - +
54C GLU* 2.9 31.3 + - + -
55C LYS* 2.9 41.0 + - + +
57C GLU* 3.1 35.3 + - + -
65C LYS* 5.8 0.8 - - + +
66C VAL* 1.3 77.7 - - - +
68C CYS* 1.3 59.8 + - - +
96C PHE* 6.3 1.6 - - + -
97C ASP 3.8 4.5 - - - +
98C VAL* 3.4 29.6 - - + +
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Residues in contact with CYS 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C VAL* 5.7 2.0 - - + -
39C MET* 3.8 27.1 - - + -
51C ALA* 3.6 19.7 - - + -
52C ARG 3.2 12.1 - - - +
53C VAL* 4.9 2.0 - - + -
54C GLU* 4.5 3.6 - - - +
66C VAL* 4.3 9.4 - - + -
67C HIS* 1.3 75.8 - - - +
69C ARG* 1.3 59.8 + - - +
70C TRP* 4.0 15.2 + - - -
96C PHE* 3.7 5.3 - - - +
97C ASP* 2.9 55.8 + - - +
98C VAL 4.7 0.9 - - - -
99C GLN* 4.7 3.6 - - - -
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Residues in contact with ARG 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ALA* 3.4 2.4 - - - -
52C ARG* 2.9 58.7 + - + +
54C GLU* 3.4 23.9 + - - +
68C CYS* 1.3 73.7 - - - +
70C TRP* 1.3 63.5 + - - +
71C TYR* 3.7 0.9 + - - -
92C LEU* 3.8 16.6 + - + +
93C SER 2.7 32.8 + - - +
94C ASP* 4.5 6.5 - - - +
95C HIS 3.6 8.5 - - - +
96C PHE* 3.4 35.6 - - + -
132C GLU* 3.6 21.8 + - - -
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Residues in contact with TRP 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C MET* 4.3 20.0 - - + -
49C TYR* 3.3 43.7 - + + -
50C VAL 3.4 21.1 - - - -
51C ALA* 3.9 13.9 - - + -
68C CYS* 4.5 12.1 - - - -
69C ARG* 1.3 73.7 - - - +
71C TYR* 1.3 64.5 + - - +
72C TYR* 4.1 12.8 - - + -
92C LEU* 4.4 1.4 - - - +
93C SER* 2.7 42.6 + - - +
95C HIS* 3.1 43.9 + + + +
97C ASP* 3.1 35.0 + - + +
99C GLN* 4.1 16.8 - - - -
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Residues in contact with TYR 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C CYS* 3.7 26.8 - - - -
49C TYR* 5.7 1.2 - - - +
50C VAL* 2.9 45.2 + - + +
51C ALA 4.0 7.4 - - - -
52C ARG* 4.0 24.0 + - + -
69C ARG 3.7 1.1 + - - -
70C TRP* 1.3 74.4 - - - +
72C TYR* 1.3 63.2 + - - +
73C ARG* 3.9 2.4 + - - +
76C GLU* 4.8 3.3 - - - +
90C LEU* 3.8 30.2 - - + +
91C PHE 3.4 15.5 - - - -
92C LEU* 3.8 36.5 - - + +
110C VAL* 3.9 26.5 + - + +
129C CYS* 4.3 7.9 - - + +
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Residues in contact with TYR 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C TRP* 4.0 9.4 - - + -
71C TYR* 1.3 75.2 - - - +
73C ARG* 1.3 66.5 + - - +
74C PRO 3.8 0.5 - - - -
76C GLU* 3.9 22.4 - - + -
77C SER 3.9 14.1 - - - +
90C LEU* 3.5 9.5 - - - +
91C PHE* 2.9 45.0 + - + +
93C SER* 3.4 33.0 - - - -
95C HIS* 3.5 26.9 - + + -
133C TYR* 3.8 26.7 - + + -
135C ALA* 3.6 17.0 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il